Contacts of the helix formed by residues 1822 - 1830 (chain B) in PDB entry 2IWO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR1822 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1859A ASP* 3.7 24.0 - - - +
1823B GLU* 1.3 71.2 + - - +
1824B ASN* 3.2 5.1 - - - +
1825B LEU* 3.0 16.7 + - - +
1826B TYR* 2.9 35.0 + - - -
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Residues in contact with GLU1823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852A GLY* 4.6 0.9 - - - -
1853A VAL* 4.0 17.2 + - - +
1859A ASP* 3.4 25.8 + - + +
1860A VAL 3.4 21.2 + - - +
1861A PRO* 3.8 10.9 - - - +
1862A ILE* 4.9 1.0 + - - +
1893A THR 4.5 4.4 - - - +
1894A GLU* 3.4 25.5 - - - +
1895A GLY* 3.0 30.6 + - - -
1896A MET 4.8 0.3 - - - +
1822B THR* 1.3 79.4 - - - +
1824B ASN* 1.3 59.1 - - - +
1826B TYR* 3.3 7.2 + - - +
1827B PHE* 3.0 37.2 + - + +
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Residues in contact with ASN1824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1894A GLU* 2.4 44.3 + - - +
1822B THR* 3.2 3.0 - - - +
1823B GLU* 1.3 77.0 - - - +
1825B LEU* 1.3 59.0 + - - +
1827B PHE* 3.4 5.3 + - - +
1828B GLN* 2.9 33.2 + - - +
1832B LEU 4.4 1.0 - - - +
1834B THR* 3.7 32.2 + - - +
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Residues in contact with LEU1825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1822B THR* 3.0 20.6 + - - +
1824B ASN* 1.3 75.1 - - - +
1826B TYR* 1.3 66.0 + - + +
1828B GLN* 3.4 10.3 + - - +
1829B SER* 3.0 22.3 + - - -
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Residues in contact with TYR1826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1857A LEU* 4.7 7.0 + - - +
1859A ASP 3.7 15.5 - - - -
1860A VAL* 3.5 29.0 - - + +
1861A PRO* 3.5 22.2 - - + -
1922A VAL* 6.3 0.9 - - + -
1923A SER* 4.9 20.4 - - - -
1822B THR* 2.9 33.8 + - - -
1823B GLU 3.3 1.1 + - - +
1825B LEU* 1.3 76.2 - - + +
1827B PHE* 1.3 62.3 + - - +
1829B SER* 2.6 29.0 + - - -
1830B MET* 3.4 15.8 + - + +
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Residues in contact with PHE1827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861A PRO* 3.6 32.3 - - + +
1884A ARG* 4.3 12.6 - - + -
1885A ILE 3.8 17.5 - - - -
1886A VAL* 4.0 23.1 - - + -
1893A THR* 3.9 11.2 - - - -
1894A GLU* 3.6 26.5 - - + -
1917A VAL* 4.5 7.6 - - + -
1823B GLU* 3.0 24.1 + - + -
1824B ASN* 3.4 7.8 + - - +
1826B TYR* 1.3 76.2 - - - +
1828B GLN* 1.3 57.4 + - - +
1830B MET* 2.9 23.0 + - - +
1831B GLY 3.2 0.3 + - - -
1832B LEU* 3.0 51.7 + - + +
1834B THR* 5.2 2.0 - - - +
1915B GLN* 4.5 4.5 - - - -
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Residues in contact with GLN1828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1824B ASN 2.9 19.8 + - - +
1825B LEU* 3.6 9.2 - - - +
1827B PHE* 1.3 74.7 - - - +
1829B SER* 1.3 62.6 + - - +
1831B GLY* 3.1 13.3 + - - -
1832B LEU 3.1 13.5 + - - +
1833B ARG* 4.1 27.3 - - + +
1834B THR 5.1 3.9 + - - +
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Residues in contact with SER1829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1922A VAL* 3.4 42.1 - - - +
1825B LEU 3.0 13.5 + - - -
1826B TYR* 2.6 24.5 + - - -
1828B GLN* 1.3 75.8 - - - +
1830B MET* 1.4 63.1 + - - +
1831B GLY 3.5 0.2 - - - -
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Residues in contact with MET1830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861A PRO* 5.0 1.8 - - + -
1884A ARG* 3.6 59.0 - - + +
1917A VAL* 4.2 22.2 - - + +
1918A ALA 3.9 23.3 - - - +
1919A GLY* 4.0 15.0 - - - +
1922A VAL* 4.7 5.2 - - + -
1923A SER* 4.5 9.0 - - - +
1826B TYR* 3.8 26.7 - - + +
1827B PHE* 2.9 13.1 + - - +
1829B SER* 1.4 83.8 + - - +
1831B GLY* 1.3 60.2 + - - +
1832B LEU* 3.5 0.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il